suppressPackageStartupMessages({
library(Seurat)
library(org.Dr.eg.db)
library(BSgenome.Drerio.UCSC.danRer11)
library(Signac)
library(knitr)
library(kableExtra)
library(dplyr)
library(ggplot2)
library(ggsci)
library(limma)
library(JASPAR2020)
library(patchwork)
library(TFBSTools)
library(motifmatchr)
library(AnnotationHub)
library(harmony)
})
options(future.globals.maxSize = 4000 * 1024^2)
int.3WT <- readRDS(file = "RDSfiles/int.neural.3WT.RDS")
p1 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.0.8", label = T, repel = T) + scale_color_igv() + NoLegend()
p2 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "Clusters", label = T, repel = T) + scale_color_igv() + NoLegend()
p1 + p2
# remove old individual cluster resolutions
int.3WT$wsnn_res.1 <- NULL
int.3WT$wsnn_res.1.5 <- NULL
int.3WT$wsnn_res.2 <- NULL
int.3WT$wsnn_res.2.5 <- NULL
int.3WT$wsnn_res.3 <- NULL
int.3WT$wsnn_res.3.5 <- NULL
int.3WT$wsnn_res.6 <- NULL
int.3WT$wsnn_res.8 <- NULL
int.3WT <- FindClusters(int.3WT, graph.name = "wsnn", resolution = 2, algorithm = 3, verbose = FALSE)
int.3WT <- FindClusters(int.3WT, graph.name = "wsnn", resolution = 3, algorithm = 3, verbose = FALSE)
int.3WT <- FindClusters(int.3WT, graph.name = "wsnn", resolution = 4, algorithm = 3, verbose = FALSE)
int.3WT <- FindClusters(int.3WT, graph.name = "wsnn", resolution = 5, algorithm = 3, verbose = FALSE)
int.3WT <- FindClusters(int.3WT, graph.name = "wsnn", resolution = 6, algorithm = 3, verbose = FALSE)
p1 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.2", label = T, repel = T) + scale_color_igv() + NoLegend()
p2 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.3", label = T, repel = T) + scale_color_igv() + NoLegend()
p3 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.4", label = T, repel = T) + scale_color_igv() + NoLegend()
p4 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.5", label = T, repel = T) + scale_color_igv() + NoLegend()
p5 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.6", label = T, repel = T) + scale_color_igv() + NoLegend()
p6 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "Clusters", label = T, repel = T) + scale_color_igv() + NoLegend()
(p1 + p2 + p3) / (p4 + p5 + p6)
Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps
saveRDS(int.3WT, file = "RDSfiles/int.neural.3WT.RDS")
Based on what I’m seeing resolution 5 might be what we want since it separates r1, r2, r1&r2, r4 and DorsNT into separate clusters. Resolution 6 only further resolves cluster 5 in res 5 (MHB) into clusters 18 and 28 in res 6.
p1 <- DimPlot(int.3WT, reduction = "wnn.umap", group.by = "wsnn_res.5", split.by = "orig.ident", label = T, repel = T) + scale_color_igv()
p1
DimPlot(int.3WT, reduction = "wnn.umap", group.by = "Clusters", split.by = "orig.ident", label = T, repel = T, ncol = 3) + scale_color_igv() + NoLegend()
as.data.frame(table(int.3WT$Clusters, int.3WT$wsnn_res.5)) %>%
tidyr::pivot_wider(names_from = "Var2", values_from = "Freq") %>%
rename("Cluster" = "Var1") %>%
mutate(Cluster = gsub(" ","",Cluster)) %>%
mutate(across(everything(), gsub, pattern = "^0$", replacement = ".")) %>%
kbl(caption = "Cell Count Orig Clusters by Res 5 clusters") %>%
kable_classic(full_width = F, "striped")
| Cluster | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHB.1 | 46 | 19 | . | 14 | . | . | . | 3 | 45 | . | . | . | 1 | . | . | . | . | . | . | 4 | . | . | . | . | 4 | . | . | . | . | 1 | . | 1 | . | . | 6 | . | 1 | . | . | . | . | 1 |
| CHB.2 | 71 | . | . | 41 | . | . | . | 1 | 3 | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | 14 | . | . | 1 | . | . | . | 4 |
| CHB.3 | . | 2 | . | 60 | . | . | . | 2 | 29 | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 1 | 1 | . | . | . | 1 | 14 | . | . | . | . | . | . | 1 |
| CHB.4 | 8 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | . | . | 1 |
| Ciliated | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | 14 | . | . | . | 44 | . | 1 | . | . | . | . | . | 1 | 1 | . | 2 | . | . |
| DorsNT&NC | . | . | 4 | . | . | . | . | . | . | . | . | . | 29 | . | . | . | . | . | . | . | 23 | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB | . | . | . | . | 2 | . | . | . | . | . | 1 | 10 | . | . | 1 | . | . | . | 35 | . | . | . | . | 16 | . | . | 1 | . | 2 | 3 | 4 | . | 5 | . | . | . | . | . | 1 | . | . | . |
| FB&eye.2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 8 | 2 | . | . | . | . | . | . | . | 1 | 15 | . | . | . | . | . | 9 | . | . | . |
| FB&eye.1 | . | . | . | . | . | 1 | . | . | . | . | . | 37 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB&eye.3 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 17 | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | 8 | . | . | . |
| FB&eye.4 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 7 | 1 | . | . | . | . | . | . | . | . | 9 | . | . | . | . | . | 4 | . | . | . |
| FB&eye.5 | . | . | . | . | . | 16 | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB&eye.6 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 17 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . |
| FB&eye.7 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 5 | 1 | . | . | . | . | . | . | . | . | 4 | . | . | . | . | . | 2 | . | . | . |
| FB&eye.8 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB.1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 35 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 1 |
| FB.2 | . | . | . | . | . | . | . | 1 | . | . | . | 26 | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . |
| FB.3 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 23 | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . |
| FB.4 | . | . | . | . | 1 | . | . | . | . | 1 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | 21 | . | . | . | . | . | . | . | . | . | . | . |
| HB.1 | . | . | 19 | . | . | . | . | . | . | . | . | . | 8 | 6 | . | 7 | 2 | . | . | . | 3 | 2 | . | . | . | 1 | . | . | . | 5 | . | . | . | . | . | . | . | 2 | . | . | 1 | 1 |
| HB.2 | 1 | . | . | 2 | . | . | . | . | . | . | . | . | . | 7 | . | . | . | 1 | . | . | 2 | 1 | . | . | . | . | . | 4 | . | 1 | . | . | . | . | 1 | . | . | 21 | . | . | . | . |
| HB.3 | 2 | . | . | . | . | . | . | 1 | . | . | . | . | . | 1 | . | . | . | . | . | . | 5 | . | . | . | . | . | . | . | . | 2 | . | . | 1 | . | . | . | . | 2 | . | . | . | . |
| MB | . | . | . | . | 11 | 2 | . | . | . | . | 1 | . | . | . | 29 | . | . | . | . | . | . | 1 | . | . | . | . | 2 | . | . | 2 | 1 | . | . | . | . | . | . | . | . | . | . | . |
| MB.1 | . | . | . | . | 36 | 1 | . | . | . | 1 | . | 1 | . | . | 34 | . | . | . | 2 | . | . | . | . | . | . | . | 4 | . | . | 2 | 12 | . | . | . | . | . | . | . | 1 | . | . | . |
| MB.2 | . | . | . | . | 31 | 21 | . | . | . | 1 | . | . | . | . | 5 | . | . | . | . | . | 1 | . | . | . | . | . | 6 | . | . | 2 | . | . | 1 | . | . | . | . | . | . | . | . | 1 |
| MB.3 | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.1 | . | . | . | . | 7 | 2 | 58 | 1 | . | 20 | . | . | 1 | . | . | 2 | . | . | . | . | . | . | . | . | . | 24 | 8 | . | . | 2 | 1 | . | . | . | . | . | . | . | . | . | 3 | . |
| MHB.2 | . | . | . | . | . | 44 | 17 | . | . | 16 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 7 | 7 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | 11 | 1 |
| MHB.3 | . | . | . | . | . | 22 | 24 | . | . | 14 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | 2 | 24 | . | . | 2 | . | . | . | 1 | . | . | . | . | . | . | 1 | 1 |
| MHB.4 | . | . | . | . | 1 | 3 | . | . | . | 24 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.5 | . | . | . | . | . | . | 4 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 16 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| NC.1 | . | . | . | . | . | . | . | 1 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 1 | . | 2 | 20 | . | . | 20 | . | . |
| NC.2 | 6 | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | 4 | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | 1 | . | 2 | 1 | . | . | . | . |
| Neuron | . | . | . | . | . | . | . | 62 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | 34 | 1 | . | . | . | 1 | . |
| r1 | . | . | . | . | . | . | 2 | . | . | . | . | . | 4 | 1 | . | 59 | 1 | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | 10 | . | . | . | 1 | . | . | . | . |
| r1&r2 | . | . | . | . | . | . | . | 1 | . | . | . | . | 22 | . | . | 1 | 4 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r2 | . | . | . | . | . | . | . | . | . | . | . | . | 3 | 5 | . | . | 59 | . | . | . | 1 | . | . | . | . | . | . | . | 1 | . | . | . | . | 23 | . | . | . | . | . | . | . | . |
| r3 | . | . | 98 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 2 |
| r4 | . | . | . | . | . | . | . | 1 | 1 | . | . | . | . | 48 | . | . | 1 | . | . | . | 23 | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | 1 |
| r5 | . | . | 1 | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | 20 | . | . | . | 20 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | 1 |
| r5.1 | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 42 | . | . | . | 1 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r5.2 | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . | . | 35 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r6 | 1 | . | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 45 | . | . | . | 37 | . | 1 | . | . | . | . | . | . | . | . |
| SC.1 | . | 68 | . | . | . | . | . | 5 | 1 | . | 42 | . | 1 | . | . | . | . | . | . | 1 | . | . | . | . | 21 | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| SC.2 | . | 40 | . | 3 | . | . | . | 2 | 1 | . | 11 | . | . | . | . | . | . | . | . | 21 | 1 | . | . | . | 16 | . | . | . | . | . | . | . | 1 | . | 1 | . | 2 | . | . | . | . | 1 |
| SC.3 | . | 4 | . | . | . | . | . | . | . | . | 21 | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . | 5 | . | . |
as.data.frame(table(int.3WT$orig.ident, int.3WT$wsnn_res.5)) %>%
tidyr::pivot_wider(names_from = "Var2", values_from = "Freq") %>%
rename("Sample" = "Var1") %>%
kbl(caption = "Cell Count Sample by Res 5 clusters") %>%
kable_classic(full_width = F, "striped")
| Sample | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HB10hpf | 27 | 43 | 19 | 10 | 20 | 39 | 18 | 7 | 5 | 22 | 55 | 37 | 9 | 15 | 31 | 7 | 2 | 1 | 32 | 10 | 11 | 4 | 56 | 4 | 21 | 10 | 15 | 4 | 3 | 19 | 6 | 1 | 36 | 1 | 36 | 2 | 22 | 27 | 25 | 23 | 16 | 5 |
| HB13hpf | 46 | 38 | 45 | 44 | 61 | 39 | 50 | 26 | 31 | 37 | 12 | 27 | 26 | 24 | 32 | 27 | 35 | 20 | 24 | 22 | 23 | 20 | 1 | 38 | 14 | 20 | 22 | 24 | 24 | 8 | 21 | 16 | 2 | 10 | 0 | 18 | 7 | 1 | 3 | 2 | 0 | 10 |
| HB16hpf | 62 | 52 | 62 | 66 | 38 | 34 | 37 | 51 | 44 | 19 | 10 | 10 | 38 | 33 | 8 | 35 | 30 | 45 | 6 | 30 | 26 | 36 | 1 | 16 | 22 | 24 | 15 | 23 | 22 | 17 | 13 | 22 | 0 | 27 | 1 | 16 | 1 | 1 | 0 | 2 | 1 | 2 |
as.data.frame(table(int.3WT$Clusters, int.3WT$orig.ident)) %>%
tidyr::pivot_wider(names_from = "Var2", values_from = "Freq") %>%
rename("Cluster" = "Var1") %>%
mutate(Cluster = gsub(" ","",Cluster)) %>%
mutate(across(everything(), gsub, pattern = "^0$", replacement = ".")) %>%
kbl(caption = "Cell Count Orig Clusters by Sample") %>%
kable_classic(full_width = F, "striped")
| Cluster | HB10hpf | HB13hpf | HB16hpf |
|---|---|---|---|
| CHB.1 | 38 | 51 | 57 |
| CHB.2 | 36 | 46 | 56 |
| CHB.3 | 24 | 38 | 52 |
| CHB.4 | . | . | 20 |
| Ciliated | . | 28 | 36 |
| DorsNT&NC | . | . | 57 |
| FB | 49 | . | 32 |
| FB&eye.2 | 35 | . | . |
| FB&eye.1 | 41 | . | . |
| FB&eye.3 | 26 | . | . |
| FB&eye.4 | 22 | . | . |
| FB&eye.5 | 19 | . | . |
| FB&eye.6 | 18 | . | . |
| FB&eye.7 | 12 | . | . |
| FB&eye.8 | 2 | . | . |
| FB.1 | . | 37 | . |
| FB.2 | . | 29 | . |
| FB.3 | . | 26 | . |
| FB.4 | . | 25 | . |
| HB.1 | 57 | . | . |
| HB.2 | 41 | . | . |
| HB.3 | 14 | . | . |
| MB | 49 | . | . |
| MB.1 | . | 37 | 57 |
| MB.2 | . | 36 | 33 |
| MB.3 | . | 30 | . |
| MHB.1 | 39 | 45 | 45 |
| MHB.2 | 37 | 35 | 33 |
| MHB.3 | 31 | 34 | 27 |
| MHB.4 | . | 31 | . |
| MHB.5 | . | 21 | . |
| NC.1 | 46 | . | . |
| NC.2 | 17 | . | . |
| Neuron | . | 37 | 63 |
| r1 | . | 39 | 41 |
| r1&r2 | . | 29 | . |
| r2 | . | 37 | 55 |
| r3 | . | 47 | 54 |
| r4 | . | 38 | 38 |
| r5 | . | 44 | . |
| r5.1 | . | . | 46 |
| r5.2 | . | . | 40 |
| r6 | . | 38 | 48 |
| SC.1 | 49 | 44 | 47 |
| SC.2 | 38 | 31 | 31 |
| SC.3 | 16 | 17 | 30 |
as.data.frame(table(int.3WT$Clusters[int.3WT$orig.ident == "HB10hpf"], int.3WT$wsnn_res.5[int.3WT$orig.ident == "HB10hpf"])) %>%
tidyr::pivot_wider(names_from = "Var2", values_from = "Freq") %>%
rename("Cluster" = "Var1") %>%
mutate(Cluster = gsub(" ","",Cluster)) %>%
mutate(across(everything(), gsub, pattern = "^0$", replacement = ".")) %>%
kbl(caption = "HB10hpf cell count") %>%
kable_classic(full_width = F, "striped")
| Cluster | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHB.1 | . | 18 | . | 1 | . | . | . | 2 | 3 | . | . | . | . | . | . | . | . | . | . | 3 | . | . | . | . | 4 | . | . | . | . | 1 | . | . | . | . | 6 | . | . | . | . | . | . | . |
| CHB.2 | 18 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 14 | . | . | 1 | . | . | . | 1 |
| CHB.3 | . | . | . | 7 | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | 14 | . | . | . | . | . | . | 1 |
| FB | . | . | . | . | 2 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | 31 | . | . | . | . | . | . | . | 1 | . | 2 | 2 | 4 | . | 5 | . | . | . | . | . | 1 | . | . | . |
| FB&eye.2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 8 | 2 | . | . | . | . | . | . | . | 1 | 15 | . | . | . | . | . | 9 | . | . | . |
| FB&eye.1 | . | . | . | . | . | 1 | . | . | . | . | . | 37 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB&eye.3 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 17 | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | 8 | . | . | . |
| FB&eye.4 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 7 | 1 | . | . | . | . | . | . | . | . | 9 | . | . | . | . | . | 4 | . | . | . |
| FB&eye.5 | . | . | . | . | . | 16 | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB&eye.6 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 17 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . |
| FB&eye.7 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 5 | 1 | . | . | . | . | . | . | . | . | 4 | . | . | . | . | . | 2 | . | . | . |
| FB&eye.8 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| HB.1 | . | . | 19 | . | . | . | . | . | . | . | . | . | 8 | 6 | . | 7 | 2 | . | . | . | 3 | 2 | . | . | . | 1 | . | . | . | 5 | . | . | . | . | . | . | . | 2 | . | . | 1 | 1 |
| HB.2 | 1 | . | . | 2 | . | . | . | . | . | . | . | . | . | 7 | . | . | . | 1 | . | . | 2 | 1 | . | . | . | . | . | 4 | . | 1 | . | . | . | . | 1 | . | . | 21 | . | . | . | . |
| HB.3 | 2 | . | . | . | . | . | . | 1 | . | . | . | . | . | 1 | . | . | . | . | . | . | 5 | . | . | . | . | . | . | . | . | 2 | . | . | 1 | . | . | . | . | 2 | . | . | . | . |
| MB | . | . | . | . | 11 | 2 | . | . | . | . | 1 | . | . | . | 29 | . | . | . | . | . | . | 1 | . | . | . | . | 2 | . | . | 2 | 1 | . | . | . | . | . | . | . | . | . | . | . |
| MHB.1 | . | . | . | . | 7 | 2 | . | . | . | 17 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | 8 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | 3 | . |
| MHB.2 | . | . | . | . | . | . | 16 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 7 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | 11 | 1 |
| MHB.3 | . | . | . | . | . | 18 | 2 | . | . | 5 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | 4 | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . |
| NC.1 | . | . | . | . | . | . | . | 1 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 1 | . | 2 | 20 | . | . | 20 | . | . |
| NC.2 | 6 | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | 4 | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | 1 | . | 2 | 1 | . | . | . | . |
| SC.1 | . | 6 | . | . | . | . | . | . | . | . | 42 | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| SC.2 | . | 16 | . | . | . | . | . | . | 1 | . | 2 | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 16 | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | 1 |
| SC.3 | . | 3 | . | . | . | . | . | . | . | . | 8 | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . |
as.data.frame(table(int.3WT$Clusters[int.3WT$orig.ident == "HB13hpf"], int.3WT$wsnn_res.5[int.3WT$orig.ident == "HB13hpf"])) %>%
tidyr::pivot_wider(names_from = "Var2", values_from = "Freq") %>%
rename("Cluster" = "Var1") %>%
mutate(Cluster = gsub(" ","",Cluster)) %>%
mutate(across(everything(), gsub, pattern = "^0$", replacement = ".")) %>%
kbl(caption = "HB13hpf cell count") %>%
kable_classic(full_width = F, "striped")
| Cluster | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHB.1 | 46 | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | 1 | . | . | . | . | 1 |
| CHB.2 | . | . | . | 39 | . | . | . | . | 3 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 |
| CHB.3 | . | 2 | . | 2 | . | . | . | 2 | 27 | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | 1 | . | . | . | 1 | . | . | . | . | . | . | . | . |
| Ciliated | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | 4 | . | . | . | 23 | . | . | . | . | . | . | . | . | . | . | . | . | . |
| FB.1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 35 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 1 |
| FB.2 | . | . | . | . | . | . | . | 1 | . | . | . | 26 | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . |
| FB.3 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 23 | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . |
| FB.4 | . | . | . | . | 1 | . | . | . | . | 1 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | 21 | . | . | . | . | . | . | . | . | . | . | . |
| MB.1 | . | . | . | . | 1 | 1 | . | . | . | . | . | 1 | . | . | 30 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | 1 | . | . | . |
| MB.2 | . | . | . | . | 28 | . | . | . | . | 1 | . | . | . | . | 2 | . | . | . | . | . | 1 | . | . | . | . | . | 1 | . | . | 1 | . | . | 1 | . | . | . | . | . | . | . | . | 1 |
| MB.3 | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.1 | . | . | . | . | . | . | 43 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.2 | . | . | . | . | . | 32 | 1 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.3 | . | . | . | . | . | 3 | . | . | . | 9 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | 1 |
| MHB.4 | . | . | . | . | 1 | 3 | . | . | . | 24 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.5 | . | . | . | . | . | . | 4 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 16 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| Neuron | . | . | . | . | . | . | . | 18 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 18 | 1 | . | . | . | . | . |
| r1 | . | . | . | . | . | . | 2 | . | . | . | . | . | 1 | 1 | . | 26 | 1 | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | 5 | . | . | . | 1 | . | . | . | . |
| r1&r2 | . | . | . | . | . | . | . | 1 | . | . | . | . | 22 | . | . | 1 | 4 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r2 | . | . | . | . | . | . | . | . | . | . | . | . | . | 4 | . | . | 30 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . | . | . | . | . | . | . |
| r3 | . | . | 44 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | 2 |
| r4 | . | . | . | . | . | . | . | 1 | . | . | . | . | . | 16 | . | . | . | . | . | . | 21 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r5 | . | . | 1 | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | 20 | . | . | . | 20 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | 1 |
| r6 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 23 | . | . | . | 15 | . | . | . | . | . | . | . | . | . | . |
| SC.1 | . | 31 | . | . | . | . | . | 3 | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 9 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| SC.2 | . | 5 | . | 3 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 21 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . |
| SC.3 | . | . | . | . | . | . | . | . | . | . | 12 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . | 2 | . | . |
as.data.frame(table(int.3WT$Clusters[int.3WT$orig.ident == "HB16hpf"], int.3WT$wsnn_res.5[int.3WT$orig.ident == "HB16hpf"])) %>%
tidyr::pivot_wider(names_from = "Var2", values_from = "Freq") %>%
rename("Cluster" = "Var1") %>%
mutate(Cluster = gsub(" ","",Cluster)) %>%
mutate(across(everything(), gsub, pattern = "^0$", replacement = ".")) %>%
kbl(caption = "HB16hpf cell count") %>%
kable_classic(full_width = F, "striped")
| Cluster | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHB.1 | . | 1 | . | 13 | . | . | . | 1 | 42 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| CHB.2 | 53 | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| CHB.3 | . | . | . | 51 | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| CHB.4 | 8 | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | . | . | 1 |
| Ciliated | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 10 | . | . | . | 21 | . | 1 | . | . | . | . | . | 1 | 1 | . | 2 | . | . |
| DorsNT&NC | . | . | 4 | . | . | . | . | . | . | . | . | . | 29 | . | . | . | . | . | . | . | 23 | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| FB | . | . | . | . | . | . | . | . | . | . | . | 10 | . | . | 1 | . | . | . | 4 | . | . | . | . | 16 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| MB.1 | . | . | . | . | 35 | . | . | . | . | 1 | . | . | . | . | 4 | . | . | . | 1 | . | . | . | . | . | . | . | 4 | . | . | . | 12 | . | . | . | . | . | . | . | . | . | . | . |
| MB.2 | . | . | . | . | 3 | 21 | . | . | . | . | . | . | . | . | 3 | . | . | . | . | . | . | . | . | . | . | . | 5 | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.1 | . | . | . | . | . | . | 15 | 1 | . | 3 | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | 23 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.2 | . | . | . | . | . | 12 | . | . | . | 15 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 6 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| MHB.3 | . | . | . | . | . | 1 | 22 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . |
| Neuron | . | . | . | . | . | . | . | 44 | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | 16 | . | . | . | . | 1 | . |
| r1 | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . | 33 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 5 | . | . | . | . | . | . | . | . |
| r2 | . | . | . | . | . | . | . | . | . | . | . | . | 3 | 1 | . | . | 29 | . | . | . | 1 | . | . | . | . | . | . | . | 1 | . | . | . | . | 20 | . | . | . | . | . | . | . | . |
| r3 | . | . | 54 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r4 | . | . | . | . | . | . | . | . | 1 | . | . | . | . | 32 | . | . | 1 | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | 1 |
| r5.1 | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 42 | . | . | . | 1 | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r5.2 | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 3 | . | . | . | 35 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| r6 | 1 | . | . | . | . | . | . | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 22 | . | . | . | 22 | . | 1 | . | . | . | . | . | . | . | . |
| SC.1 | . | 31 | . | . | . | . | . | 2 | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | 12 | . | . | . | . | 1 | . | . | . | . | . | . | . | . | . | . | . | . |
| SC.2 | . | 19 | . | . | . | . | . | 2 | . | . | 9 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . |
| SC.3 | . | 1 | . | . | . | . | . | . | . | . | 1 | . | . | . | . | . | . | . | . | 28 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
Rational: the amount of FB or FB&eye was dissection specific and not possible to precisely control.
After examining Cell Count Original Clusters by Res 5 clusters will remove clusters: 11, 18, 22, 23, 32 and 38
Will keep 29 – this has lots of cells from a variety of clusters and may be interesting Will keep 5 – this is in with MB clusters and may have been mislabeled previously.
Will also keep 30 since this more closely associated with MB clusters than FB clusters.
Idents(int.3WT) <- "wsnn_res.5"
int.3WT.subset <- subset(int.3WT, idents = c("11","18","22","23","32","38"), invert = TRUE)
DimPlot(int.3WT.subset, reduction = "wnn.umap", label = T, repel = T) + scale_color_igv()
p1 <- DimPlot(int.3WT.subset, reduction = "wnn.umap", group.by = "wsnn_res.5", split.by = "orig.ident", label = T, repel = T) + scale_color_igv()
p1
DimPlot(int.3WT.subset, reduction = "wnn.umap", group.by = "Clusters", split.by = "orig.ident", label = T, repel = T, ncol = 3) + scale_color_igv() + NoLegend()
Idents(int.3WT.subset) <- "Clusters"
HB1cells <- WhichCells(int.3WT.subset, idents = "HB.1")
HB2cells <- WhichCells(int.3WT.subset, idents = "HB.2")
HB3cells <- WhichCells(int.3WT.subset, idents = "HB.3")
p1 <- DimPlot(int.3WT.subset, group.by = "wsnn_res.5", cells.highlight = HB1cells, reduction = "wnn.umap") + NoLegend() + ggtitle("HB.1 cells")
p2 <- DimPlot(int.3WT.subset, group.by = "wsnn_res.5", cells.highlight = HB2cells, reduction = "wnn.umap") + NoLegend() + ggtitle("HB.2 cells")
p3 <- DimPlot(int.3WT.subset, group.by = "wsnn_res.5", cells.highlight = HB3cells, reduction = "wnn.umap") + NoLegend() + ggtitle("HB.3 cells")
p4 <- DimPlot(int.3WT.subset, group.by = "wsnn_res.5", reduction = "wnn.umap", label = TRUE, repel = T) + NoLegend() + scale_color_igv()
(p1 + p2) / (p3 + p4)
Since there are still a few cells which were originally called FB or FB&eye in other clusters, these labels are still in the metadata table and are still cluttering up the UMAP. So will remove all labels with “FB” in them from UMAP of cluster labels.
int.3WT.subset$fixedClusters <- int.3WT.subset$Clusters
int.3WT.subset$fixedClusters[grep("FB", int.3WT.subset$fixedClusters)] <- " "
p1 <- DimPlot(int.3WT.subset, group.by = "fixedClusters", cells.highlight = HB1cells, reduction = "wnn.umap") + NoLegend() + ggtitle("HB.1 cells")
p2 <- DimPlot(int.3WT.subset, group.by = "fixedClusters", cells.highlight = HB2cells, reduction = "wnn.umap") + NoLegend() + ggtitle("HB.2 cells")
p3 <- DimPlot(int.3WT.subset, group.by = "fixedClusters", cells.highlight = HB3cells, reduction = "wnn.umap") + NoLegend() + ggtitle("HB.3 cells")
p4 <- DimPlot(int.3WT.subset, group.by = "fixedClusters", reduction = "wnn.umap", label = TRUE, repel = T) + NoLegend() + scale_color_igv()
(p1 + p2) / (p3 + p4)
Idents(int.3WT.subset) <- "wsnn_res.5"
All.markers <- FindAllMarkers(int.3WT.subset, only.pos = TRUE)
write.table(All.markers, file = "../results/int3WT.subset.markers.res.5.txt", sep = "\t", quote = F, col.names = NA)
cellCount <- as.data.frame(table(int.3WT.subset$Clusters, int.3WT.subset$wsnn_res.5, int.3WT.subset$orig.ident)) %>%
dplyr::filter(!Freq == 0)
write.table(cellCount, file = "../results/int3WT.cellCount.res.5.txt", quote = F, sep = "\t", row.names = FALSE)
After determining cluster cell types, adding as “intClusters”
DimPlot(int.3WT.subset, group.by = "wsnn_res.5", reduction = "wnn.umap", label = TRUE, repel = T) + NoLegend() + scale_color_igv()
Idents(int.3WT.subset) <- "wsnn_res.5"
int.3WT.subset <- RenameIdents(int.3WT.subset,
"0" = "CaudHB.1",
"1" = "SC.1",
"2" = "r3.1",
"3" = "CaudHB.2",
"4" = "MB.1",
"5" = "MHB.1",
"6" = "MHB.2",
"7" = "Neuron.1",
"8" = "CaudHB.3",
"9" = "MHB.3",
"10" = "SC.2",
"12" = "r1&r2.1",
"13" = "r4.1",
"14" = "MB.2",
"15" = "r1",
"16" = "r2",
"17" = "r5.1",
"19" = "SC.3",
"20" = "r4.2",
"21" = "r5.2",
"24" = "SC.4",
"25" = "MHB.4",
"26" = "MHB.5",
"27" = "r6.1",
"28" = "Ciliated",
"29" = "Neurog",
"30" = "MB.3",
"31" = "r6.2",
"33" = "r1&r2.2",
"34" = "CaudHB.4",
"35" = "Neuron.2",
"36" = "NC.1",
"37" = "HB",
"39" = "NC.2",
"40" = "MHB.6",
"41" = "Mitochondrial")
int.3WT.subset$intClusters <- Idents(int.3WT.subset)
DimPlot(int.3WT.subset, reduction = "wnn.umap", label = TRUE, repel = T) + NoLegend() + scale_color_igv() + ggtitle("Integrated Neural Clusters")
saveRDS(int.3WT.subset, file = "RDSfiles/int.neural.3WT.subset.RDS")
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.3
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] ensembldb_2.18.0 AnnotationFilter_1.18.0
[3] GenomicFeatures_1.46.1 AnnotationHub_3.2.0
[5] BiocFileCache_2.2.0 dbplyr_2.1.1
[7] harmony_0.1.0 Rcpp_1.0.7
[9] motifmatchr_1.16.0 TFBSTools_1.32.0
[11] patchwork_1.1.1 JASPAR2020_0.99.10
[13] limma_3.50.3 ggsci_2.9
[15] ggplot2_3.3.5 dplyr_1.0.7
[17] kableExtra_1.3.4 knitr_1.36
[19] Signac_1.2.1 BSgenome.Drerio.UCSC.danRer11_1.4.2
[21] BSgenome_1.62.0 rtracklayer_1.54.0
[23] Biostrings_2.62.0 XVector_0.34.0
[25] GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
[27] org.Dr.eg.db_3.14.0 AnnotationDbi_1.56.1
[29] IRanges_2.28.0 S4Vectors_0.32.4
[31] Biobase_2.54.0 BiocGenerics_0.40.0
[33] SeuratObject_4.0.4 Seurat_4.0.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SnowballC_0.7.0 scattermore_0.7
[4] R.methodsS3_1.8.1 ragg_1.2.2 tidyr_1.1.4
[7] nabor_0.5.0 bit64_4.0.5 irlba_2.3.3
[10] DelayedArray_0.20.0 R.utils_2.11.0 data.table_1.14.2
[13] rpart_4.1-15 KEGGREST_1.34.0 RCurl_1.98-1.5
[16] generics_0.1.1 cowplot_1.1.1 RSQLite_2.2.8
[19] RANN_2.6.1 chromVAR_1.16.0 future_1.26.1
[22] bit_4.0.4 tzdb_0.2.0 spatstat.data_2.1-0
[25] webshot_0.5.2 xml2_1.3.2 httpuv_1.6.3
[28] SummarizedExperiment_1.24.0 assertthat_0.2.1 DirichletMultinomial_1.36.0
[31] xfun_0.27 hms_1.1.1 jquerylib_0.1.4
[34] evaluate_0.14 promises_1.2.0.1 progress_1.2.2
[37] fansi_0.5.0 restfulr_0.0.13 caTools_1.18.2
[40] igraph_1.2.8 DBI_1.1.1 htmlwidgets_1.5.4
[43] sparsesvd_0.2 spatstat.geom_2.3-0 purrr_0.3.4
[46] ellipsis_0.3.2 RSpectra_0.16-0 backports_1.3.0
[49] annotate_1.72.0 biomaRt_2.50.0 deldir_1.0-6
[52] MatrixGenerics_1.6.0 vctrs_0.4.1 ROCR_1.0-11
[55] abind_1.4-5 cachem_1.0.6 withr_2.4.2
[58] ggforce_0.3.3 checkmate_2.0.0 sctransform_0.3.3
[61] GenomicAlignments_1.30.0 prettyunits_1.1.1 goftest_1.2-3
[64] svglite_2.0.0 cluster_2.1.2 ape_5.5
[67] lazyeval_0.2.2 seqLogo_1.60.0 crayon_1.4.2
[70] pkgconfig_2.0.3 slam_0.1-48 labeling_0.4.2
[73] tweenr_1.0.2 ProtGenerics_1.26.0 nlme_3.1-153
[76] nnet_7.3-16 rlang_1.0.3 globals_0.15.1
[79] lifecycle_1.0.1 miniUI_0.1.1.1 filelock_1.0.2
[82] dichromat_2.0-0 polyclip_1.10-0 matrixStats_0.61.0
[85] lmtest_0.9-38 Matrix_1.3-4 ggseqlogo_0.1
[88] zoo_1.8-9 base64enc_0.1-3 ggridges_0.5.3
[91] png_0.1-7 viridisLite_0.4.0 rjson_0.2.20
[94] bitops_1.0-7 R.oo_1.24.0 KernSmooth_2.23-20
[97] blob_1.2.2 stringr_1.4.0 parallelly_1.32.0
[100] jpeg_0.1-9 readr_2.0.2 CNEr_1.30.0
[103] scales_1.1.1 memoise_2.0.0 magrittr_2.0.1
[106] plyr_1.8.6 ica_1.0-2 zlibbioc_1.40.0
[109] compiler_4.1.0 BiocIO_1.4.0 RColorBrewer_1.1-2
[112] fitdistrplus_1.1-6 Rsamtools_2.10.0 cli_3.3.0
[115] listenv_0.8.0 pbapply_1.5-0 htmlTable_2.3.0
[118] Formula_1.2-4 MASS_7.3-54 mgcv_1.8-38
[121] tidyselect_1.1.1 stringi_1.7.5 textshaping_0.3.6
[124] highr_0.9 yaml_2.2.1 latticeExtra_0.6-29
[127] ggrepel_0.9.1 grid_4.1.0 VariantAnnotation_1.40.0
[130] sass_0.4.0 fastmatch_1.1-3 tools_4.1.0
[133] future.apply_1.8.1 parallel_4.1.0 rstudioapi_0.13
[136] TFMPvalue_0.0.8 foreign_0.8-81 lsa_0.73.2
[139] gridExtra_2.3 farver_2.1.0 Rtsne_0.15
[142] digest_0.6.28 BiocManager_1.30.16 shiny_1.7.1
[145] pracma_2.3.3 qlcMatrix_0.9.7 BiocVersion_3.14.0
[148] later_1.3.0 RcppAnnoy_0.0.19 httr_1.4.2
[151] rsconnect_0.8.24 biovizBase_1.42.0 colorspace_2.0-2
[154] rvest_1.0.2 XML_3.99-0.8 tensor_1.5
[157] reticulate_1.22 splines_4.1.0 uwot_0.1.10
[160] RcppRoll_0.3.0 spatstat.utils_2.2-0 renv_0.15.5
[163] plotly_4.10.0 systemfonts_1.0.4 xtable_1.8-4
[166] jsonlite_1.7.2 poweRlaw_0.70.6 R6_2.5.1
[169] Hmisc_4.6-0 pillar_1.6.4 htmltools_0.5.2
[172] mime_0.12 glue_1.6.2 fastmap_1.1.0
[175] DT_0.19 BiocParallel_1.28.0 interactiveDisplayBase_1.32.0
[178] codetools_0.2-18 utf8_1.2.2 lattice_0.20-45
[181] bslib_0.3.1 spatstat.sparse_2.0-0 tibble_3.1.6
[184] curl_4.3.2 leiden_0.3.9 gtools_3.9.2
[187] GO.db_3.14.0 survival_3.2-13 rmarkdown_2.11
[190] docopt_0.7.1 munsell_0.5.0 GenomeInfoDbData_1.2.7
[193] reshape2_1.4.4 gtable_0.3.0 spatstat.core_2.3-0